AMBER Archive (2006)

Subject: AMBER: Trouble with ptraj closestwater in Amber8

From: Kerry P Donny-Clark (kerry_at_nyu.edu)
Date: Thu May 04 2006 - 12:29:23 CDT

Hello Amber users,
I used closestwater to strip all waters save the 100 closest to my
residues of interest (see script below). However, each water molecule's
name in each frame of the trajectory is different. This makes it very hard
to analyze distances, angels, etc as they depend on my knowing the
identity of the water molecule that I want to measure. Since the name of
one molecule changes constantly my analysis gives me a bunch of wildly
differing numbers. Is there any way to make sure one water molecule
maintains the same name throughout the trajectory?

I am using Amber8.

Here is the relevant portion of the ptraj script used:

solvent byres :WAT
closestwater 100 :390-409 first noimage

Thanks,
Kerry
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